Interpretive Summary: Soybean is the second most important cash crop in the U.S. with an estimated value of $19.8 billion. Genetically modified (GM) soybean is widely grown in the U.S. and abroad. Currently, soybean cultivars are being developed with a variety of modifications to enhance quality and productivity. It is therefore important to determine if any unintended changes occur in the soybean seed as a result of the genetic modification. We have applied a modern protein analysis (proteomics) approach in which seed proteins are separated and identified using a device called a “mass spectrometer” to determine the range of soybean seed proteins in non-GM soybean seeds. This standardized approach will provide scientists with a means to identify unintended changes that may be present in the seed of new GM soybeans.

Technical Abstract:
Proteomic technologies are currently used as an effective analytical tool for examining modifications in protein profiles for assessing the bio-safety of genetically modified (GM) crop organisms. Understanding the natural variation of soybean seed proteins is necessary to evaluate potential unintended (collateral) effects due to transgenic modifications in GM soybeans. We used two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry, and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) to separate, identify and quantify the different classes of soybean seed proteins. Sixteen soybean genotypes, including four wild and twelve cultivated genotypes, belonging to four different subgroups were used as models for protein profile evaluation. Significant variation of allergen and anti-nutritional protein profiles were observed between cultivated and wild soybean genotypes. Only minor variations in protein profiles were observed within the cultivated or wild subgroups. These results will be useful to scientists needing to compare GM and non-GM soybeans.